#!/bin/bash
a=1

java SimilarValues > SimilarValuesOutput
split -l 1000000 pdb_uniprot_map.lst.2


while read pdb alpha 
do
	
	echo $pdb
	echo $alpha
	echo $PWD
	grep -R --include="x*" "$pdb" $PWD > location
	if [ $? -eq $a ]
	then
		echo "$pdb not found"
	else
		filename="$pdb""_""$alpha"".fa"
		java SequenceFrompdb "$pdb" "$alpha"> $filename 
	
	fi
	

done < SimilarValuesOutput
